Uranium reduction and microbial community development in response to stimulation with different electron donors

Construction of an egg-like DTAB/SiO2 composite for the enhanced removal of uranium

For the past few years, the environmental safety problems of radioactive nuclides caused wide public concern. In this work, the dodecyl trimethyl ammonium bromide-modified silicon dioxide composite (DTAB/SiO₂) was synthesized for the elimination of uranium. The dodecyl trimethyl ammonium bromide can decorate the surface of the silicon dioxide and change its surface topography, which can offer more active sites and functional groups for the combination of U(VI). The removal capacity of U(VI) on DTAB/SiO₂ reached 78.1 mg/g, which was greater than that of the silicon dioxide nanopowder. In the adsorption process, the surface oxygen-containing functional groups formed surface complexation with uranium. The results may provide helpful content to eliminate U(VI) and expand the application of surfactant in radioactive nuclide cleanup.

Uranium bioremediation with U(VI)-reducing bacteria

Uranium (U) pollution is an environmental hazard caused by the development of the nuclear industry. Microbial reduction of hexavalent uranium (U(VI)) to tetravalent uranium (U(IV)) reduces U solubility and mobility and has been proposed as an effective method to remediate uranium contamination. In this review, U(VI) remediation with respect to U(VI)-reducing bacteria, mechanisms, influencing factors, products, and reoxidation are systematically summarized. Reportedly, some metal- and sulfate-reducing bacteria possess excellent U(VI) reduction capability through mechanisms involving c-type cytochromes, extracellular pili, electron shuttle, or thioredoxin reduction. In situ remediation has been demonstrated as an ideal strategy for large-scale degradation of uranium contaminants than ex situ. However, U(VI) reduction efficiency can be affected by various factors, including pH, temperature, bicarbonate, electron donors, and coexisting metal ions. Furthermore, it is noteworthy that the reduction products could be reoxidized when exposed to oxygen and nitrate, inevitably compromising the remediation effects, especially for non-crystalline U(IV) with weak stability.

Key Enzymes for Anaerobic Lactate Metabolism in Geobacter sulfurreducens

Growth of Geobacter sulfurreducens PCA on lactate was enhanced by laboratory adaptive evolution. The enhanced growth was considered to be attributed to increased expression of the sucCD genes, encoding a succinyl-coenzyme A (CoA) synthetase. To further investigate the function of the succinyl-CoA synthetase, the sucCD genes were deleted from G. sulfurreducens The mutant showed defective growth on lactate but not on acetate. Introduction of the sucCD genes into the mutant restored the full potential to grow on lactate. These results verify the importance of the succinyl-CoA synthetase in growth on lactate. Genome analysis of Geobacter species identified candidate genes, GSU1623, GSU1624, and GSU1620, for lactate dehydrogenase. Deletion mutants of the identified genes for d-lactate dehydrogenase (ΔGSU1623 ΔGSU1624 mutant) or l-lactate dehydrogenase (ΔGSU1620 mutant) could not grow on d-lactate or l-lactate but could grow on acetate and l- or d-lactate, respectively. Introduction of the respective genes into the mutants allowed growth on the corresponding lactate stereoisomer. These results suggest that the identified genes were essential for d- or l-lactate utilization. The lacZ reporter assay demonstrated that the putative promoter regions were more active during growth on lactate than during growth on acetate, indicating that the genes for the lactate dehydrogenases were expressed more during growth on lactate than during growth on acetate. The gene deletion phenotypes and the expression profiles indicate that there are metabolic switches between lactate and acetate. This study advances the understanding of anaerobic lactate utilization in G. sulfurreducens IMPORTANCE Lactate is a microbial fermentation product as well as a source of carbon and electrons for microorganisms in the environment. Furthermore, lactate is a common amendment for stimulation of microbial growth in environmental biotechnology applications. However, anaerobic metabolism of lactate has been poorly studied for environmentally relevant microorganisms. Geobacter species are found in various environments and environmental biotechnology applications. By employing genomic and genetic approaches, succinyl-CoA synthetase and lactate dehydrogenase were identified as key enzymes in anaerobic metabolism of lactate in Geobacter sulfurreducens, a representative Geobacter species. Differential gene expression during growth on lactate and acetate was observed, demonstrating that G. sulfurreducens could metabolically switch to adapt to available substrates in the environment. The findings provide new insights into basic physiology in lactate metabolism as well as cellular responses to growth conditions in the environment and can be informative for the application of lactate in environmental biotechnology.

Engineering and kinetic aspects of bacterial uranium reduction for the remediation of uranium contaminated environments

Biological reduction of soluble uranium from U(VI) to insoluble U(IV) coupled to the oxidation of an electron donor (hydrogen or organic compounds) is a potentially cost-efficient way to reduce the U concentrations in contaminated waters to below regulatory limits. A variety of microorganisms originating from both U contaminated and non-contaminated environments have demonstrated U(VI) reduction capacity under anaerobic conditions. Bioreduction of U(VI) is considered especially promising for in situ remediation, where the activity of indigenous microorganisms is stimulated by supplying a suitable electron donor to the subsurface to contain U contamination to a specific location in a sparingly soluble form. Less studied microbial biofilm-based bioreactors and bioelectrochemical systems have also shown potential for efficient U(VI) reduction to remove U from contaminated water streams. This review compares the advantages and challenges of U(VI)-reducing in situ remediation processes, bioreactors and bioelectrochemical systems. In addition, the current knowledge of U(VI) bioreduction mechanisms and factors affecting U(VI) reduction kinetics (e.g. pH, temperature, and the chemical composition of the contaminated water) are discussed, as both of these aspects are important in designing efficient remediation processes.

Responses exhibited by various microbial groups relevant to uranium exposure

There is a strong interest in knowing how various microbial systems respond to the presence of uranium (U), largely in the context of bioremediation. There is no known biological role for uranium so far. Uranium is naturally present in rocks and minerals. The insoluble nature of the U(IV) minerals keeps uranium firmly bound in the earth's crust minimizing its bioavailability. However, anthropogenic nuclear reaction processes over the last few decades have resulted in introduction of uranium into the environment in soluble and toxic forms. Microbes adsorb, accumulate, reduce, oxidize, possibly respire, mineralize and precipitate uranium. This review focuses on the microbial responses to uranium exposure which allows the alteration of the forms and concentrations of uranium within the cell and in the local environment. Detailed information on the three major bioprocesses namely, biosorption, bioprecipitation and bioreduction exhibited by the microbes belonging to various groups and subgroups of bacteria, fungi and algae is provided in this review elucidating their intrinsic and engineered abilities for uranium removal. The survey also highlights the instances of the field trials undertaken for in situ uranium bioremediation. Advances in genomics and proteomics approaches providing the information on the regulatory and physiologically important determinants in the microbes in response to uranium challenge have been catalogued here. Recent developments in metagenomics and metaproteomics indicating the ecologically relevant traits required for the adaptation and survival of environmental microbes residing in uranium contaminated sites are also included. A comprehensive understanding of the microbial responses to uranium can facilitate the development of in situ U bioremediation strategies.

Quantifying Technetium and Strontium Bioremediation Potential in Flowing Sediment Columns

The high-yield fission products ⁹⁹Tc and ⁹⁰Sr are found as problematic radioactive contaminants in groundwater at nuclear sites. Treatment options for radioactively contaminated land include bioreduction approaches, and this paper explores ^99mTc and ⁹⁰Sr behavior and stability under a range of biogeochemical conditions stimulated by electron donor addition methods. Dynamic column experiments with sediment from the Sellafield nuclear facility, completed at site relevant flow conditions, demonstrated that Fe(III)-reducing conditions had developed by 60 days. Sediment reactivity toward ⁹⁹Tc was then probed using a ^99mTc(VII) tracer at <10^-10 mol L^-1 and γ camera imaging showed full retention of ^99mTc in acetate amended systems. Sediment columns were then exposed to selected treatments to examine the effects of different acetate amendment regimes and reoxidation scenarios over 55 days when they were again imaged with ^99mTc. Here, partially oxidized sediments with no further electron donor additions remained reactive toward ^99mTc under relevant groundwater O₂ and NO₃^- concentrations over 55 days. Immobilization of ^99mTc was highest where continuous acetate amendment had resulted in sulfate-reducing conditions. Interestingly, the sulfate reducing system showed enhanced Sr retention when stable Sr²⁺ was added continuously as a proxy for ⁹⁰Sr. Overall, sediment reactivity was nondestructively imaged over an extended period to provide new information about dynamic iron and radionuclide biogeochemistry throughout realistic sediment redox cycling regimes.

Influence of bicarbonate on the abundance of microbial communities capable of reducing U(vi) in groundwater

7 experiments amended with 0, 5, 10, 15, 20, 25 and 30 mM initial concentrations of bicarbonate were conducted to investigate the influence of different concentrations of bicarbonate on the abundance of microbial communities capable of reducing U(vi) in groundwater.

Uranium Bioreduction and Biomineralization

Following the development of nuclear science and technology, uranium contamination has been an ever increasing concern worldwide because of its potential for migration from the waste repositories and long-term contaminated environments. Physical and chemical techniques for uranium pollution are expensive and challenging. An alternative to these technologies is microbially mediated uranium bioremediation in contaminated water and soil environments due to its reduced cost and environmental friendliness. To date, four basic mechanisms of uranium bioremediation-uranium bioreduction, biosorption, biomineralization, and bioaccumulation-have been established, of which uranium bioreduction and biomineralization have been studied extensively. The objective of this review is to provide an understanding of recent developments in these two fields in relation to relevant microorganisms, mechanisms, influential factors, and obstacles.

Interaction of Uranium with Bacterial Cell Surfaces: Inferences from Phosphatase-Mediated Uranium Precipitation

Deinococcus radiodurans and Escherichia coli expressing either PhoN, a periplasmic acid phosphatase, or PhoK, an extracellular alkaline phosphatase, were evaluated for uranium (U) bioprecipitation under two specific geochemical conditions (GCs): (i) a carbonate-deficient condition at near-neutral pH (GC1), and (ii) a carbonate-abundant condition at alkaline pH (GC2). Transmission electron microscopy revealed that recombinant cells expressing PhoN/PhoK formed cell-associated uranyl phosphate precipitate under GC1, whereas the same cells displayed extracellular precipitation under GC2. These results implied that the cell-bound or extracellular location of the precipitate was governed by the uranyl species prevalent at that particular GC, rather than the location of phosphatase. MINTEQ modeling predicted the formation of predominantly positively charged uranium hydroxide ions under GC1 and negatively charged uranyl carbonate-hydroxide complexes under GC2. Both microbes adsorbed 6- to 10-fold more U under GC1 than under GC2, suggesting that higher biosorption of U to the bacterial cell surface under GC1 may lead to cell-associated U precipitation. In contrast, at alkaline pH and in the presence of excess carbonate under GC2, poor biosorption of negatively charged uranyl carbonate complexes on the cell surface might have resulted in extracellular precipitation. The toxicity of U observed under GC1 being higher than that under GC2 could also be attributed to the preferential adsorption of U on cell surfaces under GC1. This work provides a vivid description of the interaction of U complexes with bacterial cells. The findings have implications for the toxicity of various U species and for developing biological aqueous effluent waste treatment strategies.

IMPORTANCE

The present study provides illustrative insights into the interaction of uranium (U) complexes with recombinant bacterial cells overexpressing phosphatases. This work demonstrates the effects of aqueous speciation of U on the biosorption of U and the localization pattern of uranyl phosphate precipitated as a result of phosphatase action. Transmission electron microscopy revealed that location of uranyl phosphate (cell associated or extracellular) was primarily influenced by aqueous uranyl species present under the given geochemical conditions. The data would be useful for understanding the toxicity of U under different geochemical conditions. Since cell-associated precipitation of metal facilitates easy downstream processing by simple gravity-based settling down of metal-loaded cells, compared to cumbersome separation techniques, the results from this study are of considerable relevance to effluent treatment using such cells.

Bioreduction of U(VI) and stability of immobilized uranium under suboxic conditions

In order to study the bioreduction of U(VI) and stability of immobilized uranium under suboxic conditions, microcosm were amended with ethanol, lactate and glucose, and incubated under suboxic conditions. During the incubation, total dissolved U in amended microcosms decreased from 0.95 mg/L to 0.03 mg/L. Pyrosequencing results showed that, the proportion of anaerobic microorganisms capable of reducing U(VI) under suboxic conditions was small compared with that under anoxic conditions; the proportion of aerobic and facultative anaerobic microorganisms capable of consuming the dissolved oxygen was large; and some of the facultative anaerobic microorganisms could reduce U(VI). These results indicated that different microbial communities were responsible for the bioreduction of U(VI) under suboxic and anoxic conditions. After the electron donors were exhausted, total dissolved U in the amended microcosms remained unchanged, while the U(VI)/U(IV) ratio in the solid phase of sediments increased obviously. This implied that the performance of bioreduction of the U(VI) can be maintained under suboxic condition.

Impact of Organic Carbon Electron Donors on Microbial Community Development under Iron- and Sulfate-Reducing Conditions

Although iron- and sulfate-reducing bacteria in subsurface environments have crucial roles in biogeochemical cycling of C, Fe, and S, how specific electron donors impact the compositional structure and activity of native iron- and/or sulfate-reducing communities is largely unknown. To understand this better, we created bicarbonate-buffered batch systems in duplicate with three different electron donors (acetate, lactate, or glucose) paired with ferrihydrite and sulfate as the electron acceptors and inoculated them with subsurface sediment as the microbial inoculum. Sulfate and ferrihydrite reduction occurred simultaneously and were faster with lactate than with acetate. 16S rRNA-based sequence analysis of the communities over time revealed that Desulfotomaculum was the major driver for sulfate reduction coupled with propionate oxidation in lactate-amended incubations. The reduction of sulfate resulted in sulfide production and subsequent abiotic reduction of ferrihydrite. In contrast, glucose promoted faster reduction of ferrihydrite, but without reduction of sulfate. Interestingly, the glucose-amended incubations led to two different biogeochemical trajectories among replicate bottles that resulted in distinct coloration (white and brown). The two outcomes in geochemical evolution might be due to the stochastic evolution of the microbial communities or subtle differences in the initial composition of the fermenting microbial community and its development via the use of different glucose fermentation pathways available within the community. Synchrotron-based x-ray analysis indicated that siderite and amorphous Fe(II) were formed in the replicate bottles with glucose, while ferrous sulfide and vivianite were formed with lactate or acetate. These data sets reveal that use of different C utilization pathways projects significant changes in microbial community composition over time that uniquely impact both the geochemistry and mineralogy of subsurface environments.

Real-time monitoring of subsurface microbial metabolism with graphite electrodes

Monitoring in situ microbial activity in anoxic submerged soils and aquatic sediments can be labor intensive and technically difficult, especially in dynamic environments in which a record of changes in microbial activity over time is desired. Microbial fuel cell concepts have previously been adapted to detect changes in the availability of relatively high concentrations of organic compounds in waste water but, in most soils and sediments, rates of microbial activity are not linked to the concentrations of labile substrates, but rather to the turnover rates of the substrate pools with steady state concentrations in the nM-μM range. In order to determine whether levels of current produced at a graphite anode would correspond to the rates of microbial metabolism in anoxic sediments, small graphite anodes were inserted in sediment cores and connected to graphite brush cathodes in the overlying water. Currents produced were compared with the rates of [2-(14)C]-acetate metabolism. There was a direct correlation between current production and the rate that [2-(14)C]-acetate was metabolized to (14)CO2 and (14)CH4 in sediments in which Fe(III) reduction, sulfate reduction, or methane production was the predominant terminal electron-accepting process. At comparable acetate turnover rates, currents were higher in the sediments in which sulfate-reduction or Fe(III) reduction predominated than in methanogenic sediments. This was attributed to reduced products (Fe(II), sulfide) produced at distance from the anode contributing to current production in addition to the current that was produced from microbial oxidation of organic substrates with electron transfer to the anode surface in all three sediment types. The results demonstrate that inexpensive graphite electrodes may provide a simple strategy for real-time monitoring of microbial activity in a diversity of anoxic soils and sediments.

Methane production from protozoan endosymbionts following stimulation of microbial metabolism within subsurface sediments

Previous studies have suggested that protozoa prey on Fe(III)- and sulfate-reducing bacteria that are enriched when acetate is added to uranium contaminated subsurface sediments to stimulate U(VI) reduction. In order to determine whether protozoa continue to impact subsurface biogeochemistry after these acetate amendments have stopped, 18S rRNA and ß-tubulin sequences from this phase of an in situ uranium bioremediation field experiment were analyzed. Sequences most similar to Metopus species predominated, with the majority of sequences most closely related to M. palaeformis, a cilitated protozoan known to harbor methanogenic symbionts. Quantification of mcrA mRNA transcripts in the groundwater suggested that methanogens closely related to Metopus endosymbionts were metabolically active at this time. There was a strong correlation between the number of mcrA transcripts from the putative endosymbiotic methanogen and Metopus ß-tubulin mRNA transcripts during the course of the field experiment, suggesting that the activity of the methanogens was dependent upon the activity of the Metopus species. Addition of the eukaryotic inhibitors cyclohexamide and colchicine to laboratory incubations of acetate-amended subsurface sediments significantly inhibited methane production and there was a direct correlation between methane concentration and Metopus ß-tubulin and putative symbiont mcrA gene copies. These results suggest that, following the stimulation of subsurface microbial growth with acetate, protozoa harboring methanogenic endosymbionts become important members of the microbial community, feeding on moribund biomass and producing methane.

Disturbed subsurface microbial communities follow equivalent trajectories despite different structural starting points

Microbial community structure, and niche and neutral processes can all influence response to disturbance. Here, we provide experimental evidence for niche versus neutral and founding community effects during a bioremediation-related organic carbon disturbance. Subsurface sediment, partitioned into 22 flow-through columns, was stimulated in situ by the addition of acetate as a carbon and electron donor source. This drove the system into a new transient biogeochemical state characterized by iron reduction and enriched Desulfuromonadales, Comamonadaceae and Bacteroidetes lineages. After approximately 1 month conditions favoured sulfate reduction, and were accompanied by a substantial increase in the relative abundance of Desulfobulbus, Desulfosporosinus, Desulfitobacterium and Desulfotomaculum. Two subsets of four to five columns each were switched from acetate to lactate amendment during either iron (earlier) or sulfate (later) reduction. Hence, subsets had significantly different founding communities. All lactate treatments exhibited lower relative abundances of Desulfotomaculum and Bacteroidetes, enrichments of Clostridiales and Psychrosinus species, and a temporal succession from highly abundant Clostridium sensu stricto to Psychrosinus. Regardless of starting point, lactate-switch communities followed comparable structural trajectories, whereby convergence was evident 9 to 16 days after each switch, and significant after 29 to 34 days of lactate addition. Results imply that neither the founding community nor neutral processes influenced succession following perturbation.

Bioprecipitation of uranium from alkaline waste solutions using recombinant Deinococcus radiodurans

Bioremediation of uranium (U) from alkaline waste solutions remains inadequately explored. We engineered the phoK gene (encoding a novel alkaline phosphatase, PhoK) from Sphingomonas sp. for overexpression in the radioresistant bacterium Deinococcus radiodurans. The recombinant strain thus obtained (Deino-PhoK) exhibited remarkably high alkaline phosphatase activity as evidenced by zymographic and enzyme activity assays. Deino-PhoK cells could efficiently precipitate uranium over a wide range of input U concentrations. At low uranyl concentrations (1 mM), the strain precipitated >90% of uranium within 2h while a high loading capacity of around 10.7 g U/g of dry weight of cells was achieved at 10 mM U concentration. Uranium bioprecipitation by Deino-PhoK cells was not affected in the presence of Cs and Sr, commonly present in intermediate and low level liquid radioactive waste, or after exposure to very high doses of ionizing radiation. Transmission electron micrographs revealed the extracellular nature of bioprecipitated U, while X-ray diffraction and fluorescence analysis identified the precipitated uranyl phosphate species as chernikovite. When immobilized into calcium alginate beads, Deino-PhoK cells efficiently removed uranium, which remained trapped in beads, thus accomplishing physical separation of precipitated uranyl phosphate from solutions. The data demonstrate superior ability of Deino-PhoK, over earlier reported strains, in removal of uranium from alkaline solutions and its potential use in bioremediation of nuclear and other waste.

Persistence of uranium groundwater plumes: contrasting mechanisms at two DOE sites in the groundwater-river interaction zone

We examine subsurface uranium (U) plumes at two U.S. Department of Energy sites that are located near large river systems and are influenced by groundwater-river hydrologic interaction. Following surface excavation of contaminated materials, both sites were projected to naturally flush remnant uranium contamination to levels below regulatory limits (e.g., 30 μg/L or 0.126 μmol/L; U.S. EPA drinking water standard), with 10 years projected for the Hanford 300 Area (Columbia River) and 12 years for the Rifle site (Colorado River). The rate of observed uranium decrease was much lower than expected at both sites. While uncertainty remains, a comparison of current understanding suggests that the two sites have common, but also different mechanisms controlling plume persistence. At the Hanford 300 A, the persistent source is adsorbed U(VI) in the vadose zone that is released to the aquifer during spring water table excursions. The release of U(VI) from the vadose zone and its transport within the oxic, coarse-textured aquifer sediments is dominated by kinetically-limited surface complexation. Modeling implies that annual plume discharge volumes to the Columbia River are small (<one pore volume). At the Rifle site, slow oxidation of naturally reduced, contaminant U(IV) in the saturated zone and a continuous influx of U(VI) from natural, up-gradient sources influence plume persistence. Rate-limited mass transfer and surface complexation also control U(VI) migration velocity in the sub-oxic Rifle groundwater. Flux of U(VI) from the vadose zone at the Rifle site may be locally important, but it is not the dominant process that sustains the plume. A wide range in microbiologic functional diversity exists at both sites. Strains of Geobacter and other metal reducing bacteria are present at low natural abundance that are capable of enzymatic U(VI) reduction in localized zones of accumulated detrital organic carbon or after organic carbon amendment. Major differences between the sites include the geochemical nature of residual, contaminant U; the rates of current kinetic processes (both biotic and abiotic) influencing U(VI) solid-liquid distribution; the presence of detrital organic matter and the resulting spatial heterogeneity in microbially-driven redox properties; and the magnitude of groundwater hydrologic dynamics controlled by river-stage fluctuations, geologic structures, and aquifer hydraulic properties. The comparative analysis of these sites provides important guidance to the characterization, understanding, modeling, and remediation of groundwater contaminant plumes influenced by surface water interaction that are common world-wide.